Oh please. If there are any "creationists" out there who are running scared, they need not do so. The new article [by Chris Mooney] is titled "You Share 98.7 Percent of Your DNA with This Sex-Obsessed Ape," referring, of course, to the precious bonobo, a chimp-like ape famous for its progressive sexual habits. Just by itself, the genetic similarity between us and apes such as the bonobo is supposed to be of knockdown importance.

But what else would anyone expect, whether on a model of Darwinism, intelligent design, or creationism? Apes and humans are similar in many ways, and you don't need Darwinian evolution to see this.

This is a common argument from the IDiots. They assume that the intelligent designer created a model primate and then tweaked it a little bit to give chimps, humans, orangutans, etc. That's why the genomes of these species are so similar.

Unfortunately for them, there's a bit more to it than that. Their model of intelligent design also has to account for the fact that humans are more similar to chimps/bonobos than to gorillas and all three are about the same genetic distance from orangutans. This sequence data correlates with the fossil record over a period of about 10-15 million years.

If evolutionary theory (population genetics) is correct, and if David Klinhoffer and chimps/bonobos actually evolved from a common ancestor, then we should observe a correspondence between the percent similarity of Klinghoffer and chimps and the predicted number of changes due to evolution.

Let's see if it works.

The human and chimp genomes are 98.6% identical or 1.4% different. That difference amounts to 44.8 million base pairs distributed throughout the entire genome. If this difference is due to evolution then it means that 22.4 million mutations have become fixed in each lineage (humans and chimp) since they diverged about five million years ago.

The average generation time of chimps and humans is 27.5 years. Thus, there have been 185,200 generations since they last shared a common ancestor if the time of divergence is accurate. (It's based on the fossil record.) This corresponds to a substitution rate (fixation) of 121 mutations per generation and that's very close to the mutation rate as predicted by evolutionary theory.

Now, I suppose that this could be just an amazing coincidence. Maybe it's a fluke that the intelligent designer introduced just the right number of changes to make it look like evolution was responsible. Or maybe the IDiots have a good explanation that they haven't revealed?

Or maybe they're just IDiots who don't know what they are talking about.

Here's what Klinghitler wrote: "None of this is news. Now, let us reason together. As Ann Gauger says in the new documentary The War on Humans, the ballyhooed genetic similarity between apes and humans refers only to protein-coding DNA, as opposed to species-specific non-protein-coding DNA. The latter, formerly dismissed as "junk," is now increasingly understood to be vital to life."

So Klinghitler and Ann Gauger, supposedly a scientist-- she of the green screen lab-- are now claiming that the 98.7% similarity only refers to the protein-coding part of the genome. Of course it refers to all sequenceable DNA, which is overwhelmingly non-coding DNA.

This IDiot now refers to non-coding DNA as "species specific", meaning I suppose that its similarity between humans and chimps is zero percent! What a liar.

Klinghitler doubles down on lies: "Sharing a high percentage of protein-coding DNA with bonobos, chimps or orangutans, higher than we share with bovines, for example, is simply what common sense would lead anyone to expect."

His whole argument boils down to, "But whatever you observe, that can also happen by magic too."

Yes, I've noticed this too. Creationists (the objection to evidence of common ancestry is mostly a creationist argument, not an ID argument) love to harrumph that "the difference between humans and chimps is not 1.23% but Much Bigger Than That".

But you have put your finger on the issue: OK, accepting their figure, whatever it is, what then is the difference between humans and gorillas? Between humans and orangs? Gibbons? Macacques? Marmosets?

They basically run away when you start talking about that. They basically can't handle common descent, except by coming up with theological conspiracy theories.

(the objection to evidence of common ancestry is mostly a creationist argument, not an ID argument)

Except that, Behe notwithstanding, they almost always take every opportunity to cast doubt on common ancestry, Klinghoffer providing just the latest example. You're quite right, there is no reason in theory why common descent should be incompatible with ID. However, since IDiots have yet to form a consistent hypothesis of their own and instead spend all their time trying to find flaws with evolutionary theory, they are compelled to deny common descent. Anything they can do to try the give the impression they know better than actual scientists, they'll do.

Where did you get that 27.5 years per generation? I would frankly be surprised if humans and chimps turned out to have the same generation time, even averaged over each entire lineage. I'm also wondering if the human and chimp branches are actually of the same length. I seem to recall that the human branch is actually somewhat longer than the chimp branch. Where, also, do you get the 98.6% figure? 98.77 is the figure from the chimp genome paper.

Finally, as a systematist I would put much less weight on genetic distances than on the good old nested hierarchy: we get one tree of primates (allowing for a predicted amount of lineage sorting) regardless of what genetic region(s) we use as data.

I'm always wondering about generation times. How were your numbers determined? It isn't the easiest thing to do and requires a lot of raw data (age of parent at birth of child for many data points). If chimps and humans are really that close, you probably don't need to consider differences millions of years ago. But I would have thought the differences would be greater.

John B, I sincerely doubt we share 97% sequence identity with mice. I would like to see a reference for that, but I don't expect you'll deliver.

There are several reasons why the 98.7% similarity between humans and apes is important, one of which Larry was very, very clear about in his post and which you seem to not to have grasped, even remotely. Please read the post before asserting the numbers have no relevance.

Another good point was made by John Harshman, and you seem not to have grasped that above.

So let's repeat.

1. The 98.7% similarity between humans and chimps is close to what we would estimate numerically given that the fossil record shows we diverged 5-6 million years ago, generation times are 20~30 years for humans or chimps, mutation rate is about ~130 mutations per generation. It's a simple, simple, simple high school level calculation, i.e. way too hard for the smartest Intelligent Design proponent in the world.

2. It is not just that humans and chimps are similar, but that they have a recognizable pattern of both similarity and difference, a pattern which is called a unique nested hierarchy. Many, many species, when compared against each other (not just human and chimp) form a unique nested hierarchy, commonly called a tree of life. This doesn't work for intelligently designed technologies: if you compare many, many artifacts, like cars and airplanes and segways, their pattern of similarities and differences will not form a unique nested hierarchy. We know from experiment and observation that common descent with slow, gradual changes forms a unique nested hierarchy, and we know from observation that intelligent design does not.

3. We know that this similarity can never be explained by function or functional constraints, because we know from experiments that most mutations are neutral, and there is enormous "wiggle room" in DNA, meaning that the exact same biochemical functions could have been achieved with enormously greater differences in DNA. The DNA that has the most functional constraints-- protein-coding DNA-- can be mutated at most positions with NO change in biochemical function. If you mutated in the right places, you could create an organism that looked and functioned exactly like a human but less than 50% similarity to human DNA. The 98.7% similarity is way, way, way beyond any constraints due to function.

4. Species with similar lifestyles and similar functional constraints can have very different DNA. A killer whale has a very similar lifestyle to a shark, but its DNA is much, much closer to the DNA of a hippo or, for that matter, any even-toed ungulate. The tree kangaroo has a lifestyle like a monkey, but its DNA is much, much closer to that of a kangaroo or wallaby. The koala has a lifestyle like a sloth but its DNA is much, much closer to the DNA of a kangaroo or the tiny marsupial monito del monte from South America. Many, many other such pattern can be compiled.

Why should the DNA difference between a killer whale and a shark be very much larger than the DNA difference between a chimp and a human?

However alike to primates inside and out is still NOT biological or genetic scientific evidence for common descent.its just seeing likeness and REASONING that it could ONLY be from common descent.this might be a insightful intelligent conclusion (its not) but its not scientific investigation.As the kids say its just lines of reasoning devoid of practical evidence.its just a hunch.SO why not another to cancel that hunch.Why not simply God gave man, a unique being, the best body on the planet for our happiness and driving cars?!All bodies are in a simple spectrum of likeness and so we could only be in the spectrum too unless weirdly special in our bodies.We are the only being that rents another beings body type.I desire to find 99% likeness with primates because it could only be this way.YET its not evidence or a hunch we are related from a ancestor. Not evidence.Evolutionism has seen a hunch and not seen the absence of evidence to justify the hunch based on scientific methodology.Its not science comparing man and apes. Whatever is true.

"Why not simply God gave man, a unique being, the best body on the planet for our happiness and driving cars?!"

Ladies and gentlemen: the fine tuning argument.

1. Look out the window and you'll see there are cars parked all around us. 2. Monkeys, cats and trees can't drive cars, only people can drive cars. 3. The only possible explanation for this is that God created us to drive cars.4. No, there's no such thing as car factories. Well, OK, there is. It changes nothing. There are car factories *now*, but how did people know God's plan for cars unless God made the first car? See? 5. Therefore gay sex is destroying America.

The theory of evolution holds that all life is related, evolving from the first single celled life 4 - 3 billion years ago. If that theory is true, what we should find is a nested hierarchy - which is what we find. Genomic sequencing shows relatedness between living species today in varying degree - based on the length of time since they diverged on branches within the hierarchy. The evidence from genetic research correlate well with evidence from geolgy and paleontology. Is all that evidence irrelevant, coincidental and without relevance? Let creationists answer such questions!

That is what we should find if the ToE and nested hierarchies are consistent with the facts - and they are! Robert's theory is that DNA is irrelevant. He doesn't believe that there is an unbroken chain of genetic relatedness over generations back in time, his own genetic relatedness to his parents is just a coincidence, a special case.

Darwin thought the monkeys of South-America were farther related from humans than the old-world monkeys. That was long before the fact of continental drift was established, showing that the continents split apart about 30 million years ago. Now we know that the separation of the continents started about 30 million years ago and the same timing of separation between those species is what the genetic evidence suggested even before the double helix was discovered.

Robert believe a wolf gave birth to a thylacine. In his world a human might as well birth a marsupial.

Well, actually the separation of South America from Africa started much, much more than 30 million years ago. About six times that, if I recall. It's actually a bit of a mystery just how primates got to South America (and hystricomorph rodents too, about the same time).

Evolutionary theory does NOT predict that all life descends from a single common ancestor. If we were to find a strange form of cell tomorrow that was not similar to other life forms, evolutionary theory would not be falsified. Common ancestry is a fact (an observation) not a theory.

Larry, you are right. When I was a student, it was commonly said that life had originated one or a few times. That was what Darwin had said too. But in that same decade became clear how similar the molecules of all cells were, especially DNA and the protein synthesis machinery. It became widely agreed that all of that could only have come about if there was only one origin of life ancestral to present-day organisms.

So evolutionary theory has not always predicted that life had one common ancestor.

@LawrenceAMoran:There are some weird bacteria which actually have a different DNA code from the standard one. See them here: https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=c I think these could be those "strange types of cells" you are looking for...I don't think it disproves evolution though - if life evolved once why not more than once with different codes? (PS the probabilities of life evolving even once have been calculated as so close to zero for me to have serious doubts, but others obviously believe it happened at least once.)

OK will do but off to bed now it's 3am here in the UK - and I didn't want you to think I was stumped by your question! Looking forward to continuing tomorrow.

Yes I am aware of the size of the differences in the codes, nevertheless they are different and incompatible. (ouch! you did it again: "in fact can be clearly seen to have evolved..." that's a "were you there?" moment if ever there was one, but I will agree "the codes might have evolved from each other".)

How do you explain the evolution of the different codes? Isn't it a bit of a problem to have codes "evolving" from the standard code? How does that work? How do organisms remain alive while the code is being changed? Interested to hear your view on that.

My views are the standard ones. Notice that variant codes appear only in species with small genomes. It's possible, through pure chance, for some rarely used codon to become unrepresented. A mutation in the translation of that codon would be entirely neutral, and later appearances of that codon could then be selected. You could look this up, you know.

"Pauline",, who says she is a genetics student at Cambridge, spews ignorantly:

You are right that the evidence of nested hierarchy supports evolution but it also supports creationism's idea of "kinds" with microevolutionary adaptation within those kinds.

Hey, cool. So I guess that means, by the evidence cited by Larry above, that humans, chimps, gorillas, and orangutans are all of the same created "kind". Maybe you should go explain that to your IDiot colleagues. Except Behe, who already admits this to be the case.

Pedro asks: "How do you calculate the probabilities of an outcome when you don't know the details of a process?"Pedro can you give an example of a process that generates information? Natural selection is not an option since we are talking about the first self replicating unit. If not then, you just need to estimate the probability of the components of a rudimentary cell self assembling. Douglas Axe estimated this probability to 10E40,000 or as Pauline expressed it "close to zero". Now remember that the maximum number of events in the observable universe (i.e. all particles interacting at Planck time since the Big Bang) is about 10E140.

Pedro, I've seen a few theories about how the first self replicating unit came in to existence but non proposing a process that actually adds information. Therefore if you do it in one or 10E9 steps is irrelevant mathematically the probability is still not better than 10E40,000.

Exactely. That's because we don't know what the processes involved are and we can only speculate. Therefore, no probabilities can be calculated. Axe and Hoyle's calculations are useless because no one proposed such a scenario. Without a detailed model no probabilities can be calculated. It's Probabilities 101.

As for adding information, I made a post in this thread about it:

It is a logical impossibility for all mutations to degrade information. Mutations can reverse themselves, you see. If the mutation changing A into B causes a loss of information, then the reverse mutation from B back to A must represent a gain of information

Where did that "information" come from?

If your question is how did the first genes originate, we don't know. NO probabilities can be calculated without a clearly defined model. Apparently Creationists already know the answer, like when Newton wrote that God stabilized the orbits of the planets. I prefer to search for real answers, like Laplace did.

Didn't you know Pedrito that pulling numbers out of their asses is ok if they are creationists trying to make evolution look impossible? No, no, no, no. Don't complain. Creationists are on the side of "God", you see? That gives them special privileges, like pulling probabilities out of their asses. If they say so it is so. They don't need no clearly defined models!

Pedro, maybe I wasn't clear enough. I was challenging you to give an example of a naturalistic process that could add information and that predates the biological evolution, which I agree can add information within the available probabilistic resources.

Any event channeling energy from some form into another that produces energy with some resulting organization would be adding information by definition.

I'll give you a spectacular example. A meteorite hit the region of Sudbury, Canada long ago (billions of years ago). The impact caused a rise in temperature, a crater and faults and crevices were created by the impact, and, because different minerals have different melting temperatures, metals flowed into those crevices and solidified there. The metals became organized and can be extracted from that place. Talk about tornadoes in a junkyard forming airplanes!

Yes. That's information Andy. Think about it this way. If we had to build machines to organize the metals that way, it would require from us a lot of energy and thinking. A lot of information! With that idea in mind you might be able to start understanding the relationships between information, energy, organization, etc.

All natural Andy. Oh that was spectacular, but day to day things like that happen at much smaller scales (and much larger but harder-to-explain scales). A bit difference in properties plus energy flow can go a long way about organizing and semi-organizing all kinds of stuff, clays, minerals, metals, crystals, etc. These can then cascade and cause organization and semi-organization of other stuff, etc, etc, etc. We observe those things every day Andy. But I should not have to explain this to you. You claim to be an engineer and therefore you should understand the relationships between energy, work, information, etc. Right?

God gave up on primates, He went back to his first love, beetles, He is still creating beetles, as new ones turn up all the time, , how many primates, and how many Ladybirds. He even created a beetle with a cannon, which must have been created, after Gunpowder was invented.

It's true that not all IDiots are stupid. Some are just incredibly dishonest. Not a single one of them is able to understand the scientific evidence in favour of evolution and/or is willing to acknowledge that evidence. As such, scorn ridicule and insults are the most appropriate responses to their proaganda. They deserve no more respect than flat earthers or Holocaust deniers.

I see you have fallen for Ken Ham's idea that there are two types of science, only one of them real. But in fact origins science is as observationa as anythingl: we see in the current world things that tell us about the past, including both fossils and DNA sequences. And don't try to equate evolution and creation; only one of them fits the evidence, and it isn't bias to point that out.

It's true that not all IDiots are stupid. Some are just incredibly dishonest. Not a single one of them is able to understand the scientific evidence in favour of evolution and/or is willing to acknowledge that evidence.

Well, at least one is: Todd Wood. He understands the scientific evidence very well. In fact, better than many working scientists. He is absolutely honest on why he is a Creationist and why he doesn't accept Evolution: Faith, pure and simple. He will be the first one to tell you that there is nothing wrong with TE. See this post:

...we can only hypothesise, make predictions and compare probabilities of competing theories.

Best get started. Once you are finished calculating the probability of life arising from natural chemical and physical processes, you will need to multiply that probability by the probability that something supernatural somehow directed it to happen in a specific way and sequence.

I'm kind of interested, though, Pauline, in your claim that scientific knowledge does not exist and cannot be attained; that there are only differing opinions based on one's "worldview". Could you, perhaps, describe to us what "Christian chemistry" looks like? Or Buddhist physics, or Jewish astronomy?

Sorry? I never said that scientific knowledge does not exist. (Hope not! I got a science degree...) I said observable science could be repeated and tested in a laboratory and the science of origins could only ever be investigated by comparing probabilities (seeing which hypothesis the scientific evidence fits best.) @John Harshman Yes the distinction that Ken Ham makes is useful, but neither he nor I said that one kind is "unreal". Do you also think weather forecasting is unscientific because it's not 100 % accurate? All I'm saying is that some parts of science cannot ever be proved 100% - that doesn't make them unscientific or unreal. The trouble is not the evidence (creationists, IDers and Evolutionists all look at the same fossil record), but their interpretation of the evidence is viewed through their world view and each side sees how it fits their own hypothesis better. Hope that clarifies what I meant. By the way, if you were really asking what "Christian" science looks like then have a read here: http://en.wikipedia.org/wiki/List_of_Christian_thinkers_in_science but I suspect you were just having a dig which is a shame.

@SRM: why would I have to multiply the first probability of life occurring naturally without God with the probability of supernatural events? You only multiply probabilities of events that BOTH happen and these two are mutually exclusive...

Pauline, what has occurred on this planet is obviously chemistry. If god had some role in the matter, then he is obviously a chemist. Positing the role of a god is neither a simplification nor a mutually exclusive alternative.

Yes the distinction that Ken Ham makes is useful, but neither he nor I said that one kind is "unreal".

No, it isn't useful, and yes, he says that historical science is unreal. That's his point. "Observational" science is the real, useful kind, while historical science is just guessing. His mantra is "Were you there?"

Of course, you may disagree with him. But I don't think you do, really.

Do you also think weather forecasting is unscientific because it's not 100 % accurate? All I'm saying is that some parts of science cannot ever be proved 100% - that doesn't make them unscientific or unreal.

In fact, no parts of science can ever be proved 100%. Science doesn't deal with proof. Some parts, however, can be confirmed with close enough to certainty for all practical purposes. Common descent of humans and chimps is one of those parts.

The trouble is not the evidence (creationists, IDers and Evolutionists all look at the same fossil record), but their interpretation of the evidence is viewed through their world view and each side sees how it fits their own hypothesis better. Hope that clarifies what I meant.

No, it merely repeats what you said before. You were wrong then too. I reject your notion of symmetry between creation and evolution. Creationists don't look at the evidence at all; they pick what they like and ignore or distort the rest. You are merely repeating Ham's party line. I doubt you can defend it.

"It's true that not all IDiots are stupid. Some are just incredibly dishonest. Not a single one of them is able to understand the scientific evidence in favour of evolution and/or is willing to acknowledge that evidence."

...may I introduce myself? I am an "IDiot" who is able to understand the scientific evidence in favour of evolution, I have a Natural Science degree from Cambridge University, specialising in Genetics in the 3rd year. I'm willing to acknowledge that evidence in favour of evolution exists: Radiocarbon dating; fossil sequences; speciation; homology; Tiktaalik; Archaeopteryx; gene duplication....I just think that most of the evidence quoted "for evolution" is actually evidence for ADAPTATION (microevolution) not macroevolution and the evidence against evolution is more compelling. As do over 800 Ph.D. scientists who have signed the document "Dissent from Darwin". Read about it here: http://www.dissentfromdarwin.org/index.php So I don't think statements like "Not a single one of them is able to understand the scientific evidence in favour of evolution" get any more believable however many times you and Richard Dawkins repeat it.

Sorry, all your degree establishes, if anything, is that you aren't ignorant. You might still be stupid. And the rest of the post seems to incline in that direction.

Those 800 Ph.D. scientists (few of whom are named Steve, incidentally) are mostly not biologists -- many aren't even scientists. And if you read what they signed a bit more carefully, you will note that it isn't a rejection of evolution at all.

But you do indeed seem ignorant of the evidence for macroevolution, so it's hard to decide between stupidity and ignorance. Then again, why do we have to choose?

Why do you resort to being rude and abusive? Surely if you were confident your arguments were robust you could simply debate with me scientifically?

I have called you neither stupid nor ignorant, but I believe you are as wrong as you believe I am.

I'm really disappointed with Creationists IDers and Evolutionists alike who resort to slagging each other off and say ridiculous things like "all Creationists don't understand the science" or "all people who believe in evolution are stupid" .

I know what those scientists signed and I am also aware of the risk of research fund withdrawal they faced by signing it. Many more are too scared to sign. So maybe more evolution sceptics are called Steve afterall ;-) Luckily, scientific truth isn't based on popularity - I wasn't trying to prove that more scientists doubt evolution than believe it, I was just demonstrating that the sentence: "Not a single one of them is able to understand the scientific evidence in favour of evolution" is very probably unlikely given the names and qualifications on the list. Have you actually read the list? "Many" aren't scientists? Really? Here is the official, accurate data:

Signers of the Scientific Dissent From Darwinism must either hold a Ph.D. in a scientific field such as biology, chemistry, mathematics, engineering, computer science, or one of the other natural sciences; or they must hold an M.D. and serve as a professor of medicine. Signers must also agree with the following statement:

"We are skeptical of claims for the ability of random mutation and natural selection to account for the complexity of life. Careful examination of the evidence for Darwinian theory should be encouraged."

So repeating Dawkins' assertion that "many of them aren't even scientists" doesn't help our mutual search for Truth. (See? I'm assuming you aren't stupid or ignorant.)

As the questions in my degree examination weren't recall questions, I'm afraid my degree does establish that I'm not stupid. Sorry about that.

So how about you telling me some of the evidence that you personally find compelling to support macroevolution. Mutations that increase information would be nice (increase not duplicate). Who knows - you might convince me. I have an open mind.

Irrational childish belief, pure and simple. He will be the first one to tell you that there is nothing wrong with TE, except that it is flat wrong.

There, fixed it for you.

That's the point. He's honest because he recognizes that there is no problem with TE. He doesn't accept it simply because of his faith and not because of any inherent problem with the theory from a scientific point of view. He is not trying to convince anyone that evolution is false as far as purely scientific arguments go. But he CAN't accept it, no matter how strong the scientific evidence, because his faith doesn't allow it. So he has faith it must be wrong, somehow. A honest creationist.

So not one example of a mutation that increases information but lots of childish abuse? And sorry about my capitals - I haven't yet worked out how to change my font. Come on - that's an open invitation to call me stupid (or ignorant if you yourself know the difference) (but please let me know how to get italics because that looks more friendly.) I had to ask my daughter if using "@" was rude! Ha Ha Ha. Yes I am actually quite old and I can laugh at myself along with you but I am willing to learn. Don't any of you want to send me some interesting articles you have found which helped your understanding of evolution?@Steve "obsessed with degrees and other trappings of authority" - isn't it funny how many of you keep repeating that IDers are all scientifically ignorant. When I produced evidence against that, instead of engaging with me because I might understand, you attacked me claiming I am "obsessed with degrees". So what possible response would have encouraged you to engage with me on an adult to adult basis?PS Why don't you like ellipses? Not sure of your definition of ra...ndom though.

Pauline, engineers and MDs aren't scientists. You should read more of this blog. And you will note that the statement says nothing about rejecting macroevolution. You should read what you do read more carefully.

Please stop with the standard creationist nonsense if you want anyone to believe that you aren't stupid. "Increase information"? First, define "information". By any standard definition of the term, it's easy; any insertion increases information.

As I've said before, the major evidence for macroevolution lies in comparisons of DNA sequences, largely the fact that they agree on phylogeny.

So not one example of a mutation that increases information but lots of childish abuse?

In the immortal words of Jason Rosenhouse:

It is a logical impossibility for all mutations to degrade information. Mutations can reverse themselves, you see. If the mutation changing A into B causes a loss of information, then the reverse mutation from B back to A must represent a gain of information (p. 65).

To get italics write: <i>italic text</i> and, after you post it, it will look like this: italic text.

Gene duplication is gain of information. It might be beneficial or not, but it is gain in information. Creationist have a very hard time understanding what information means, which leads to ignorant discussions about information "gain."

Let me try and demonstrate for the sake of education: in order to describe a duplication, we have to use at least one bit of information more than it would take to describe a single element. While this does not actually measure the information added to there system, it is a way to help us understand that a duplication increases the information in the system at least by one bit. Of course, things are more complicated than that in reality, which goes beyond merely bit-compressed descriptions, and the information added should be much more than one bit. Yet it should be clear from this "compression" that information cannot but increase when something is duplicated.

If you want novelty I can tell you that changing the specificity of a protein from one thing to another similar-but-not-identical specificity indeed is a novelty. Something that was not happening is now happening even if that is similar to something that was happening before. Now, out many of those together and you will see that as functions diverge, the "novelty" should increase.

I hope that helps. Before you come up with more questions I should say this: we have given you enough information to learn that you have been terribly misinformed by your creationist sources. Why do you insist on posting more of that crap? Why not start by checking if there's already answers to that crap, or else, at the very very least, present the crap with more caution about its potential significance? For example, what about avoiding such damning and [ignorance/stupidity]-loaded statements as "punctuated equilibrium was proposed to keep belief in evolution"?

You are quite right. his is no place for someone seeking the Truth objectively. After this post I'm off. Pity you all missed an opportunity to do what you all espouse you want - educating the ignorant.I am not an expert in many issues discussed here and I have learned (unfortunately few things on the few occasions I was spoken to politely) but to answer the question "were you there?" Well actually I was there when: "punctuated equilibrium was proposed to keep belief in evolution" so don't go changing history to suit your own point of view. It was proposed with absolutely no known process just because it had to be true if evolution wasn't to be challenged.If you are not allowed to challenge evolution without being bullied then where will science end up?

Oh Steve you are a dear. You really should be more careful whilst you're bulling others and trying to score points. After Newton and the demise of Cambridge Charles Darwin attended Christ's College Cambridge (actually I believe he got chucked out for not being clever enough!)Thanks for that. Made my day.

Well actually I was there when: "punctuated equilibrium was proposed to keep belief in evolution" so don't go changing history to suit your own point of view. It was proposed with absolutely no known process just because it had to be true if evolution wasn't to be challenged.

I doubt that you were there because you completely ignore the data that came with the proposal of punctuated equilibrium. data that showed the process in a well preserved and nicely carefully studied fossil record. I ask again: did you actually study those fossils? Did you go with Gould and/or Eldredge to see those fossils? Punctuated equilibrium was proposed because the data on those particular groups of fossils showed those periods of stasis followed by those relatively-quick speciation/radiation events. They showed those transitions. Punctuated equilibrium was not proposed to account for lack of data, but as an observation of well presented fossil records.

Really, that one finished my patience. One thing is to repeat lies found in creationist web sites or other forms of creationist propaganda. The excuse could be your unawareness of those being lies. Quite another thing is to repeat the lie as if you truly knew the facts to be so. If you did not know about the data behind the proposal, you can't say that you were there.

@Negative Entropy: "I ask again: did you actually study those fossils? Did you go with Gould and/or Eldredge to see those fossils?"

Why do you keep asking me if I went with Gould and held his fossils? Is that the only set of people who you believe are capable of understanding? Do Gould's fossils have some magical supernatural power to bestow intelligence on people so only those who actually saw or touched Gould's fossils could ever understand punctuated equilibrium? So you believe in the supernatural eh?I'm very jealous of you though because I wish I HAD been there like you were (you must have been there yourself or you wouldn't be so stupid to have implied that only people who had could possibly understand it.)

So you truly lack the basic intelligence to understand the point I'm making.

In short: Punctuated equilibrium was based on the observation of fossils that showed stasis punctuated by bursts of radiation and speciation events. Those bursts were evidenced by "transitions" and all that stuff in a well preserved, carefully studied, and abundant group of fossils.

I keep asking if you were there with Gould and/or Eldredge because you are insisting that punctuated equilibrium is just an idea to keep belief in evolution. If so, then that means that you were there and you witnessed first-hand that Gould and Eldredge, and Mayr before them, did not have any data. That one good or bad day they just decided to "invent" punctuated equilibrium to "keep belief in evolution." Hey, I just got an idea! Let's invent punctuated equilibrium! This way we can keep belief in evolution! Sure! Let's do so! Let's publish this idea. Will reviewers ask for any data? Nah! All reviewers must swear to keep faith in evolution so there will be no questions. That's right! OK, let's send the manuscript!

Did you get that now? Or maybe I should agree that lutesuite was being too kind at thinking that you are stupider than a sack of doorknobs?

What's even more to the point is that human chromosome 2 has telomeres in the middle where they don't belong and 2 centromeres. This is just what one would expect if 2 ape chromosomes fused together at sometime in the past and, in fact, if the fusion was not observed, the hypothesis that apes and humans had a common ancestor would be in serious difficulty.

"if the fusion was not observed, the hypothesis that apes and humans had a common ancestor would be in serious difficulty." well the actual fusion was NOT observed - we can only observe the results (the 2 centromeres and central telomeres) and surmise that they might have come about by fusion. That's exactly what I've been talking about up and down this post. The probability this came about by fusion might be 99.99% but it will always be a hypothesis and never a testable scientific fact.

I'd put a few more 9s on that, but your point is correct. Similarly, electrons can't be observed either. We can only see their effects. Electrons will always be a hypothesis and never a testable scientific fact. Right?

There really is no difference between the evidence for electrons and the common ancestry of apes and humans. You and Ken need to realize that.

@John HarshmanExcellent point! I do realise that but I can't speak for Ken, unfortunately.Are electrons "a testable scientific fact"? Well I agree it's a fact that there is something called an electron - the effects and behaviour of electrons can be repeatedly tested in the lab. But we don't exactly know what an electron IS (exactly what subatomic particles it's made up of and what holds it together). Will we ever be 100% sure of this? I don't think so because we can only observe the effects of electrons and not the electrons directly. But maybe if we got to a point where we could isolate all the subatomic particles and "create" an electron from these and compare it to a real electron we would be getting close.What a great analogy. It's obviously a scientific fact that the Earth and all life on it has an origin, but we can never be 100% sure of how it happened.

I think this is all a little sidetrack though. The important distinction between your two examples is that an electron is an object we can study in the present. Evolution is a PROCESS which is being put forward as an explanation of an HISTORICAL EVENT. Even if we observed macroevolution today (isn't it funny how no-one has - even in yeast which has been reproducing for over 4,000 years and is still yeast?) even then we couldn't be 100% sure that this was the process Life began on Earth...It's a bit like a crime. You can investigate the crime scene but without an eye witness you can never be 100% sure whodunnit. That's why juries are instructed to decide "beyond reasonable doubt" and not that they must have 100% proof. There is always doubt.So I agree with you that my point is correct.

The IDcreationist incredulity with respect to accepting microevolution, but not accepting DNA and the fossil record as evidence of macroevolution, is conceptually equal to accepting that steps can exist but that to imagine a staircase amounts to an irrational extrapolation.

Strangely enough, the people with this problem are almost always exclusively religious.

OK, if we had found a random smattering of steps up the staircase the existence of a staircase would be a probable interpolation, but if we had found lots of steps on the first floor and then lots on floor 100, then we might instead think that these were 2 small sets of steps with no evidence for steps all the way up. Maybe there was an elevator between floors 2 and 99?The fossil record shows large numbers of fossils that are similar, or adaptations within a kind or species and big differences between species. If evolution were true, then we would expect to see a lot more fossils with intermediate homologies. "Missing links" is a misnomer - I would expect all fossils to be on a sliding scale of change with no specific species being distinguishable. Punctuated equilibrium is just an attempt to explain the fossil record and maintain belief in evolution - but the mechanism isn't well established so it's a fudge.Where are the fossils of giraffes with short necks evolving into the current species? Where are the fossils of feathers evolving? We have plenty of fossils of scaled animals then "whoosh!" fully formed feathers...???

The fossil record supports some aspects of evolution theory (eg simpler fossils in older rock) but you have to admit that there are also some suspicious aspects which cause doubt (trilobite eye complexity, evidence for catastrophic burial, polystrate fossils of trees, Cambrian explosion). Not that any of these disprove evolution, I'm just saying it isn't unreasonable for some people to have doubts.

It's not strange that people who doubt evolution are mostly religious because evolution is currently the only theory being put forward that explains life on earth without supernatural intervention. Reject evolution and you kind of need a God unless you believe in aliens like Francis Crick -I mock you not - apparently scientists have discovered several new "Goldilocks" planets this week so watch that space - so to speak ;-)

Have you actually read the work of Gould and/or Eldredge? Have you examined the fossils that they examined? They worked on specific groups of fossils, well preserved and so abundant that they did show speciation events nicely. They found species being anatomically static for longer whiles than they would be changing, radiating, speciating. They have graphs and such showing what they found. They noticed lots of stasis and bursts of speciation events ("bursts" relative to the stasis times, because the bursts still took long times to happen, only they look quick compared to the stasis times). OK, if you knew this you would not say that:

"Punctuated equilibrium is just an attempt to explain the fossil record and maintain belief in evolution"

Obviously you took that from some creationist propaganda. Science is not done that way. Science is not proposed and performed as excuses to "maintain belief in evolution." So, if you are seriously a scientist as you claim, you are far from understanding how science is done.

With this example and most other comments you made I am convinced that you don't take your ideas from scientific sources, that you don't rely on scientific thinking. You rather take them from creationist propaganda. Therefore, despite your degrees, you are no scientist. Sorry.

Where are the fossils of giraffes with short necks evolving into the current species?

Seriously? Giraffes? You know that there's a google don't you?

Where are the fossils of feathers evolving? We have plenty of fossils of scaled animals then "whoosh!" fully formed feathers...???

Seriously seriously? For a while I was sick/tired of the number of fossils reported in the scientific literature with feathers like this, feather-like structures like that, feathers lacking this, feathers already showing that, dinosaur imprints showing feather-like stuff like that, micrographs revealing that the feather-like structure of such fossil such and such, and you missed all of that action? How come?

Again. Why on Earth do you rely on creationist propaganda if you are supposed to be a scientist?

If you want to convince anyone here that you are neither stupid nor ignorant, you will have to stop regurgitating widespread creationist nonsense. We can't see electrons; we can only study their effects. The same is true of macroevolution, and there is no difference. The invisible past is analogous to the invisible tiny. (And, by the way, electrons are not made of other particles. Leptons are unitary objects.)

I notice, also, that you seem not even to know of the existence of molecular data. You should know that the best and most voluminous evidence for macroevolution comes from comparison of DNA sequences among species.

Fossils are secondary. Others have pointed out some of your problems with them, but I will note that your expectation of smooth change at a constant rate fits neither modern ideas nor Darwin's.

Pauline wrote: " but if we had found lots of steps on the first floor and then lots on floor 100"That's not what we find. We have steps 1 through 5, 7 and 9, 15 and 20, 31 through 38 etc. etc.

The differences are relatively tiny, we have many fossils that bridge the gaps, the DNA sequences of different species can easily be aligned and relationships inferred with a high statistical significance.

Your argument is like claiming this building project should be abandoned because the ends will never join up: Bridge over Sydney harbour.

Basically you have done exactly what my analogy attempted to show: Denied the obvious relationship by claiming the staircase cannot exist despite us having found a significant fraction of the steps and regurgitated classic IDcreationist lies about DNA and the fossil record.

Your position is seemingly maintained through a mix of personal confirmation bias, appeals to your personal incredulity and misrepresentation of the evidence. It isn't based on reason.

Apparently it is just way too much for you to imagine that evolution could ever bridge the gap between any two steps in this transition: Whale fossil record, even given millions of years, while at the same time you have no problem accepting that the Wolf-Chihuahua transition could happen in a few thousand.

Thanks Pedro - finally some useful information! I have educated myself as you suggested. That's really interesting that scientists now believe that feathers didn't evolve from scales - that claim had always made me very suspicious and now it makes much more sense. I noticed that the evidence for the very first feathers was the most lacking: "little information is available on the ontogenetic development of early feathers." Do you know of any research that covers this stage (maybe not yet as these references were all very recent)? If feathers didn't evolve from scales then where did the DNA information to make feathers originate? Does anyone have any hypotheses? This stage would be most vulnerable to the "increase in information" argument from IDers. The term "evolutionary novelties" isn't very informative - practically, the DNA base pairs and information coded into them has to come from somewhere along with all the regulatory genes to control the development of the feathers (I read in the article that the latter could have been borrowed from other processes - do we know which processes use the same regulatory genes?)Thanks again.

There are also more than a dozen genera of extinct giraffids, some with relatively short necks (like the modern okapi), some with long necks, and some intermediate (Bohlinia, Samotherium). Jesus Christ, Pauline, with a degree from Cambridge (you mean the University of Cambridge, UK, right?) you might be expected to be able to check such basic facts for yourself.

Andry wrote: "Rumraket, you need to get up to-date on the "proto-whale" fossil record, a lot has happened since 1998. Just as an example: Rodhocetus is now believed neither to have had fluke nor flippers..."

So what? That changes nothing with respect to my argument. Which "gap" is an unreasonable extrapolation in the whale fossil record, to you, in light of the DNA and fossil evidence? Why's the staircase in doubt, at all?

From what pit of religiously motivated confirmation bias are you going to extract more irrational denial?

@PiotrYou mean that Palaeotragus (short necked) around in the early Miocine didn't evolve into Samotherium (short necked) in the middle Miocine and then into Okapia (short necked)? How is Samotherium an intermediate neck length giraffe between Okapi and Giraffe?Also, I thought both Bohlinia. adoumi and Bohinia attica had as long a neck as Giraffa (and B. attica has since been reclassified as Giraffa attica - so long necked.)I'm no giraffe expert - I could be wrong - just asking so don't swear.

Sorry to disappoint you Steve but I have no testosterone, I am only here to learn. I really want to know if there are any intermediate length necked giraffes. If there are, then there are; if not then there aren't. I'm not here to gloat whoever is right or wrong - isn't that how science is supposed to be conducted? Or have you forgotten?

Andy wrote: "Rumraket, whale evolution is a very shaky staircase indeed"No it isn't, this is just more denial being offered.

"and if you cannot show the gradual evolution of whales then the whole ToE is on shaky ground."Non-sequitur fallacy. Even if we couldn't, that would not follow or even be implied.

But regardless we CAN show the gradual evolution of whales, so your fallacious appeals to denial are irrelevant. The fossils are there, multiple of them have transitional features, the relationship implied is congruent with the one inferred from DNA.

All you have to offer here is the classic creationist tactic of pointing to the "gaps" between the individual fossils and saying "look, more gaps".

Rumraket, here is a link showing you what ties the Pakicetus to the Cetaceans. Let me know if you find that to be solid evidence.

http://140.220.1.9/DEPTS/ANAT/Thewissen/pdf/2004NummelaEAlNature.pdf

In figure 2, on the first page, you can easily see that sound transmission mechanism for Pakicetus is very similar to that of land mammals, only the medial synostosis between periotic and tympanic bone is missing. In Cetaceans and Pakicetus this synostosis is absent and is homologous to a gap between these bones. This gap, as strange as it sounds, is the basis for connecting Cetacea and Artiodactyla.

@Pauline: Even different species of Palaeotragus had different neck lengths. Palaeotragus germaini had a remarkably long neck. This is from the description of Samotherium in Harris, Solounias and Geraards (2010): "Neck and limbs elongate". And the following quotation is from Mitchell and Skinner (2003):

Throughout the giraffid fossil record there is clear evidence ofprogressive limb and neck elongation. Limb and neck elongationbegan with the prerequisite structural changes seen in theLeptomerycids, but it is in the palaeotragines that giraffe-likelimb and neck elongation seems to gain momentum. Samotheresand Bohlinia continued the elongation at a faster rate.

They are all giraffe experts, unlike some non-giraffe experts who have pontificated on the subject, such as the German creationist/IDiot, "Expelled" martyr, and Jehovah's Witness Dr. Wolf-Ekkehard Lönnig. A plant geneticist by training, he nevertheless published a booklet on giraffid (non)evolution three years ago. Much of the cdesignproponentsist lore concerning giraffes can be traced back to his opus.

Andy wrote: "This gap, as strange as it sounds, is the basis for connecting Cetacea and Artiodactyla."Well sure, it's what puts it within Cetacea, but not the only shared derived feature. It's just that the other shared derived features aren't unique to Cetacea (which is why they both group within mammals and all that). And then you're ignoring that the morphological evidence is congruent with the DNA evidence.

Also your link doesn't work.

It really is laughable how creationists are willing to accept microevolution, ala the Wolf-Chihuahua, in a few thousand years. But they get a brain aneurism when it comes to macroevolution over millions.

Apparently they're fine accepting that mutations and recombination can slightly shift the position of the nostrils or eyes, slightly change the position, size or angle of the joints and limbs. Slightly change coloration or camouflage patterns, slightly alter behavior like mating or feeding strategies. Slightly adjust adaptation to countless kinds of environmental factors. All this they can accept can happen in a relatively short time, but somewhere out there, there's some mysterious, magical barrier that prevents this kind of change from being able to simply continue over millions of years. A few mutations here, a few mutations there, but they'll never add up to a thousand, much less a million. It just won't ever happen.

Why not? Where is the magic barrier that prevents this kind of change from accumulating? What is it that prevents you from simply accepting that the compartive DNA studies and fossil transitions in such a simple way really implies that these observed processes not only CAN be extended into even greater degrees of change, but did happen over geological timescales?

Andy, you haven't been paying attention. Rumraket has already answered your question. They share numerous common derived features of artiodactyls, placentals, mammals, tetrapods, vertebrates, etc., plus at least one defining feature of Cetacea on top of that. Since Pakicetus is close to the base of the cetacean family tree, you can't expect it to share many uniquely cetacean features with more derived proto-whales, precisely because those "modern" features (like flukes and flippers) originated in a lineage to which pakicetids don't belong.

Furthermore only a few million years supposedly separate Pakicetus and Basilosaurus so there should be many shared features, derived or otherwise.

There are lots of shared features. What I think you are trying to say is that, given the relatively short time between the divergence point and the appearance of true basilosaurids, you would not expect the latter to have too many derived features not shared with "basalmost" cetaceans. But why? A few million years + extremely strong selective pressures (in a radically new environment) = many adaptative changes.

Andy wrote: "Ok, so what derived features does Pakicetus and Basilosaurus share?"

All the defining features that put both of them within: Eukaryota, Animalia, Chordata, Gnathostomata, Tetrapoda, Mammalia, Cetacea and Archaeoceti.

Now, you can go into each of those groupings and find all the homologous traits they both share that make them both fit into those groups and the many unlisted subgroups within them.

What, you think the taxonomists could have just placed it anywhere they wanted in the tree of life, but the only thing it shared with all the other organisms that made it possible to put it in some specific location was the inner ear, and that the rest of it's features were just some mess with no similar structures in any other organism?

So Rumraket, let me try to summarize your best evidence for whale evolution: proto-hippos and proto-whales both belong to the kingdom animalia and share features such as a pair of eyes. Is that correct?

The best evidence for whale evolution (and, more generally, for the position of any taxonomic unit in the larger family tree) is a nested hierarchy of homologies reflecting shared evolutionary innovations (morphological as well as molecular). If A is closely related to B, they exclusively share some (not necessarily many) common innovations not found in other groups, but they also have in common many other traits inherited from more distant ancestors and shared with more distant reletives. Please don't pretend it's something you can't grasp.

Oh sorry, seemed to me that was the game you and Rumraket were playing...so then give me some good examples of shared features between Pakicetus and Basilosaurus to prove your point. I can think of at least one off hand but, but still as you know analogous structures does not necessarily mean a common origin, so a few more would be great for two animals separated by so little time and yet so very different.

At this stage, I wonder whether it would just be best to ask IDers what evidence would count against ID? If we see patterns of evidence that sit perfectly with evolution, all an ID proponent has to do is say "the designer made it look like that" and thus they neutralise the evidence for evolution. But since a theory that explains everything explains nothing, shouldn't the IDers be focusing instead on what evidence would not fit the ID? Otherwise all they have is a pseudoscience feeding off real evolutionary biology rather than science of their own. And correct me if I'm wrong, don't IDers aspire to a scientific explication of design theory?

@Diogenes: The trouble with insulting others is that you leave yourself open to ridicule. You said: "This IDiot now refers to non-coding DNA as "species specific", meaning I suppose that its similarity between humans and chimps is zero percent! What a liar." Well with only 4 base pairs it's just not possible for any 2 reasonable lengths of DNA to have zero percent similarity so I'm guessing that he didn't mean that. Also, even if he has made a mistake that doesn't mean he is lying (a deliberate untruth.) How would you feel if I attacked you and said you were lying when you said: "The DNA that has the most functional constraints-- protein-coding DNA-- can be mutated at most positions with NO change in biochemical function." This is a mistake you have made (I think you exaggerated your point by inserting the word "most" (which means almost all)) but I would never call you a "liar"...Respect please!

Also, even if he has made a mistake that doesn't mean he is lying (a deliberate untruth.)

No, but it would mean he has no real knowledge of molecular biology, and therefore should STFU.

How would you feel if I attacked you and said you were lying when you said: "The DNA that has the most functional constraints-- protein-coding DNA-- can be mutated at most positions with NO change in biochemical function."

I think he would feel that you have no idea what you're talking about. Most mutations in protein coding regions ARE neutral. Is a direct consequence of the genetic code. And this is not even taking into account that many changes in aminoacids themselves won't affect protein function. It's the reason why people try to introduce mutations (for knockdowns) in the sequence corresponding to the active site instead of anywhere else.

So there is no room in scientific discussion for mistake? Come off it! This is what's wrong with the Creation/ID/evolution debate (aka bloodbath) Mistakes and people willing to make them are the best source of creativity and discovery. Are you really suggesting that debate should be silenced as only the experts should talk and everyone else has to STFU? Do you really expect me to believe that you have never made a scientific mistake or misunderstood some scientific concept in your life? @lutesuite I don't know whether to be more shocked to hear that I'm a Creationist or that my dictionary is lying to me. What exactly is your definition of "most"?

Don't be foolish. Do you think anyone with a decent knowledge of genomics would make such a basic idiotic mistake? An on top of that someone who sees himself as "correcting" the "mistakes" of a scientific theory? Are you for real?

OK that's enough. I don't see myself as trying to "correct" anything. I'm out to debate evidence with polite intelligent people who know what words like "most" mean. What a disappointment. And stick "Pauline" into Google you sexist idiot.

You know, Ann Gauger, who has a PhD in Biology, and who writes books on how TE is wrong and Evolution is wrong, but who doesn't even know that the 98.7% similarity between humans and chimps refers to the ENTIRE genome, not just the protein-coding part. This is the level of ID "scientific" arguments, and the level of their biological knowledge. Either that or they're LYING. Doesn't look pretty either way.

"I'm no giraffe expert - I could be wrong - just asking so don't swear."

When people "just" ask, they do not first STATE A PROPOSITION in support of their viewpoint that relies solely on their own ignorance (or more likely the regurgitated ignorance of others), only to later backpedal to "I'm only asking bro I ain't no expert!"

Jesus fucking Christ... do you not see how sleazy and dishonest you are being?

I don't mind being wrong. Do you?Your own definition (the first line was sufficient thank you) states thatmost = superlative of many. If you also look up "superlative":In grammar, the superlative is the form of an adverb or adjective that expresses a degree of the adverb or adjective being used that is greater than any other possible degree of the given descriptor

then you have "almost all" Ta Da!But seriously. Did you really have to type in all that crap including irrelevant definitions? You and I both know that "most" means "almost all" but why not just return to sanity (if you can find the way) and answer this:

Did you really mean to say that only mutations at the active sites will cause a change in biochemical function? Is that really true? I understand that some point mutations will still code for the correct amino acid, but if it doesn't then won't the wrong amino acid cause the protein to fold differently and affect its shape which will in turn affect its function?Try REALLY REALLY hard to answer without insulting me - go on! you can do it!

Rolf AalbergYour nests are not evidence for evolution.If a creator made from a common blueprint all biolog as he made a common blueprint for physics THEN it also would show like dna for like parts.Why not?We having like DNA to apes is not evidence of common descent. Even if true. Its just reasoning from a presumption.Another presumption kills the evidence claim.We all have eyes and so all creatures get the same store number for eyes. Yet its not evidence for common descent of a original eye type. Its just reasoning from likeness.DNA is only showing dna of types of life. It doesn't show connections. Thats a hypothesis that its likeness shows this.Evolutionists fail in the science methodology here and fail imagination.All biology should have like dna as close as its alike IF created from a single equation.Its a option and Darwin even had to debunk it. It crossed his mind.

Monkeys in south america are only a mystery because of evolutionary biogeography concepts.Its not a mystery but rather shows they are wrong once again.The monkey simply walked over to North America and south along with armidillos, boas, and heaps of other critters now extinct.The monkeys survived extinction because they lived in trees just like the sloths. Sloths survived for this reason while perishing elsewhere where they lived in abundance. This migration happened before the "ice age".

OK so I know that you are expecting some rabbit out of a hat that you can easily dismiss as rubbish, but please read this with an open mind. These are calculations by scientists who believe in Evolution not IDers or Creationists so they have no hidden agenda. I think they are interesting - I'm not attempting to persuade you to reject evolution as you are clearly happy with that - I just think that the evidence against should have equal airing to uphold objectivity in Science.

J.H.S. Haldane. 1957. The cost of natural selection. J Genetics 55: 511-524.Haldane calculated that if two species differ at 1,000 loci, and the mean rate of gene substitution is one per 300 generations, these changes will take at least 300,000 generations (6 million years for man taking 20 years per generation). So the geological time scale (Earth being only 4,540,000,000 years old) is too short for such processes to explain the changes in 3 billion loci needed for microbe to man evolution.Man and chimp differ by at least 150 million nucleotides, that would take 900,000,000,000 years (that’s older than the Earth just for pre-chimp to man!) – estimates for natural selection could only account for 1,000 of these. The rest would have had to have been fixed by random genetic drift creating millions of nearly neutral deleterious mutations – he suggested that this would have made us extinct.ReMine 1993, 2005 has extensively reviewed this problem (“Haldane’s Dilemma”) using an entirely different mathematical formula and he obtained identical results.Kimura, M. 1968. The Neutral Theory of Molecular Evolution. Cambridge University Press. P27.Kimura realised that all evolutionists of his time were evoking too much selection for too many loci. He calculated that to maintain the population number and still carry out mutation substitutions, each parent must leave 3.27 million offspring to survive and reproduce. Instead of questioning evolution, he proposed that most genetic information must be irrelevant and that evolution must be independent of selection! This shows the danger of clinging to the worldview of Evolution too tightly and not being open to other possibilities.It’s interesting that these calculations have been known for many decades but the public have never been told. Too much is at stake – if evolution is not true then without a naturalistic alternative we only have supernatural hypotheses left. So scientists keep it secret. ...to be continued...

In addition to your other problems, you don't realize that "differ by at least 150 million nucleotides" doesn't mean 150 million mutations. That figure (and where did you find it?) must be considering each base in an indel as a difference; but each indel, no matter how long, is a single mutation. Humans and chimps differ by only 35 million point mutations.

And you have picked the wrong blog to claim that junk DNA doesn't exist.

The answer to your question was clearly stated in my first paragraph: J.H.S. Haldane. 1957. The cost of natural selection. J Genetics 55: 511-524. He's an evolutionist so go and be rude to him instead of me.

"OK so I know that you are expecting some rabbit out of a hat that you can easily dismiss as rubbish, but please read this with an open mind"

It's been read before, or slightly altered versions of it certainly have. You do not understand what the person you indirectly quote is even saying. It is pure rubbish, and demonstrates that if you somehow got a degree related to biology, you sure as hell didn't learn anything along your journey.

That last paragraph at the end was the most extreme form of bullshit. I guess the bumblebee flew through supernatural means back when we did not have the knowledge to understand how it could achieve flight.

I see Pauline has flounced, but has she actually left? Announcing you're going to leave because everyone has been mean to you is a common creationist trope. But then not actually leaving is common too.

Pauline, in case you're still around: you implied that Kimura's idea that most DNA is evolving neutrally (i.e. is junk) was a desperate attempt to save evolution in the face of the data. Your disagreement with Kimura is logically equivalent to a claim that there is no junk DNA (or at least a very small amount). You really should be able to see this without me explaining it to you. Your unwillingness to own up to your claims is one reason people here think you're being dishonest. Hiding behind J. B. S. Haldane is more dishonesty; he was writing long before we had much data on junk DNA.

It’s interesting that these calculations have been known for many decades but the public have never been told. Too much is at stake – if evolution is not true then without a naturalistic alternative we only have supernatural hypotheses left. So scientists keep it secret.

Yes, hundreds of thousands of scientists worldwide signed a non-disclosure agreement, under penalty of death, against publishing scientific data and keeping stuff secret.

Muller, H.J 1950. Our load of mutations. Amer. J. Human Genetics 2: 111-176. “it becomes perfectly evident that the present number of children per couple cannot be great enough to allow selection to keep pace with mutation rate of 0.1... to make matters worse (if it is) anything like 0.5..., our present practices would be utterly out of line with human requirements.” So Muller calculated that if the mutation rate was as high as 0.5, then early man could not have evolved but actual known rates are 200 – 600 higher than the figures he was using.Also: J.V. Neel, et al. 1968. The rate with which spontaneous mutation alters the electrophoretic mobility of polypeptides. PNAS 83:389-393. “The implications of mutations of this magnitude for population genetics and evolutionary theory are profound.” A.S. Kondrashov. 1995. Contamination of the Genome by very slightly deleterious mutations: Why have we not died 100 times over? J. Theor. Biol. 175: 583-594. “I show in agreement with Tachida (1990) that VSDMs can cause too high a mutation load – the conditions under which the load may be paradoxically high are quite realistic.”M.W. Nachman & S.L Crowell, 2000. Estimate of the mutation rate per nucleotide in humans. Genetics 156: 297 – 304. “The high deleterious mutation rate in humans presents a paradox” – the genetic load would be intolerable in man. (These rates are now thought to be 10 – 30 fold higher!)

So when Diogenes patronises:

"So let's repeat.

1. The 98.7% similarity between humans and chimps is close to what we would estimate numerically given that the fossil record shows we diverged 5-6 million years ago, generation times are 20~30 years for humans or chimps, mutation rate is about ~130 mutations per generation. It's a simple, simple, simple high school level calculation, i.e. way too hard for the smartest Intelligent Design proponent in the world."

it's kind of hard to take. He might eventually be proved correct and all these geneticists proved wrong but let's discuss with respect for each others' views.Interested in your views as always!

Wow, Pauline. 1950! 1967! Cutting edge stuff! You think maybe there has been some further scientific work done on this in the over half-century since then? What do you think? Does your computer have a search engine? I hear there's this one called "Google" that people seem to use a lot. Whichever one you're using seems only able to find creationist bullshit, so I'd suggest switching.

You've been reading too much Walter ReMine and forgetting to read the criticism. Google (and that "degree" of yours) is your friend. Start with this journal so that you can catch up to the 21st century:

A very serious question Pauline: why won't you read and understand that creationist propaganda is not a good source for scientific information? I showed you a few examples where you were evidently misinformed. Why didn't you check before sprouting more and more of that shitty creationist propaganda? Is there a point in clarifying stuff for you? Where's that scientific degree of yours? Is that degree just for the show?

Yeah, you'd think there would be someone in the Cambridge genetics department qualified to correct some of "Pauline's" basic misunderstandings Surely Cambridge doesn't use creationist websites as its primary teaching source..

You really have the attention span of a flea don't you?I'm not at Cambridge. I left in the 1980's hence my stupid and ignorant attempt at re-engaging with the subject, unfortunately with a gang of self-righteous bullies.@Pedro: ""Pauline" couldn't care less what you answer" - you're quite the expert aren't you? Go look at my most recent post where I thanked you for your help. I called you a gentleman. My mistake.

Negative Entropy you oxymoronic fool: "A very serious question Pauline: why won't you read and understand that creationist propaganda is not a good source for scientific information?"The answer should be obvious when you review your tone and rudeness - why would anyone pay any attention to you?

@Pedro: ""Pauline" couldn't care less what you answer" - you're quite the expert aren't you? Go look at my most recent post where I thanked you for your help. I called you a gentleman. My mistake.

I'll give you the benefit of the doubt. But going by my previous experience at dealing with internet posers pretending to be asking honest questions and searching for honest answers, I won't be keeping my hopes high. I hope you understand, if you're really honest.

Another piece of advice: use Google. Every single one ofyour questions have been answered ad nauseam in one form or another in other blogs. There's also plenty of relevant information in free-access web articles. I gets really tiresome when new people come here asking the same shit over and over again, and the vast majority isn't even remotely interested in answers, just plucking wholes. I'll give you the benefit of the doubt you're not one of them (for now).

Crikey Pedro, you have almost calmed me down.OK I now understand that some stupid internet "posers" (I didn't know that word either) may have pretended to ask honest questions but what use would that give them? Would they wait for you to say something then copy and paste a quote mine or something? Look I'm old and trying to get acquainted with my first love - Genetics. Yes I've read ID texts but I am not a faithblind Creationist. I have also read Dawkins thoroughly and to be honest my inclination towards ID has something to do with the man's dangerous arrogance. I've encountered more of the same on this blog. I stupidly mistook the "Sandwalk" as a site where I might walk alongside scientists with different views and get a more balanced view of current Genetics.Someone makes a huge generalisation about all IDers not understanding science; I give my credentials hoping to change their mind about me at least and I get bullied for being obsessed with degrees! Are there any adults apart from you on this site or has the battle claimed their minds?

With regards to Google, when I was at University I went on a Fortran course LOL. I Google my shopping but never use it as a serious research tool. I know of so many mistakes in Wiki that I steer clear of it. Are you advising me that it's good to use such a search engine rather than asking real people who could chat about stuff? How sad but I now see your point. Is everyone just out to win an argument rather than seek the truth? Is that why people quickly accuse others of lying? Personally I don't lie (well not about science stuff ;-) . I might be ignorant of some things but why lie? If my God does exist I have nothing to fear from Evolutionary theory (some of my friends are Christians who believe in evolution and they have no problem with it.)

Thank you for giving me the benefit of the doubt. I have learned a few interesting things and have a few links to check out but I would have learned so much more if your colleagues had been more human - their behaviour has been the most convincing evidence that some humans at least have indeed descended from the primates.

I have also read Dawkins thoroughly and to be honest my inclination towards ID has something to do with the man's dangerous arrogance.

Dawkins is only useful for layman wanting to get a very general, sanitized idea of what evolution is. Otherwise, you'll just be learning about TE circa the 1960's. You won't learn anything deep about modern Molecular Evolution from Dawkins.

I know of so many mistakes in Wiki that I steer clear of it. Are you advising me that it's good to use such a search engine rather than asking real people who could chat about stuff?

Asking real people is better, but not online at forums in which said people have been repeating the same answers for ages, answers that can be found elsewhere easily. So yes, Google is recommended. You would have got your answer about feather evolution in 2 seconds. Then you can search for more details, specially on scientific papers, or maybe you can find a blog from someone who is a specialist on your topic of interest and ask him/her. Wikipedia isn't perfect, but it does contain references, so you can confirm the statements, so no problem.

If my God does exist I have nothing to fear from Evolutionary theory (some of my friends are Christians who believe in evolution and they have no problem with it.)

No one here cares if you are a believer or not, as long as you keep to the science.

The answer should be obvious when you review your tone and rudeness - why would anyone pay any attention to you?

After careful and years-to-years of looking for, studying, and studying and searching, and studying again, loads and loads of fossils, noticing some patterns, scientists could propose, based on those patterns, something about the tempo of evolution, and call their proposal "punctuated equilibrium." Yet, it sure is not rude at all to dismiss all that work and say that they proposed punctuated equilibrium just to keep belief in evolution. Sure. That's not rude at all.

Pauline, I doubt that your problem is mere ignorance. You have convinced me that you're dishonest. You ignore the work behind punctuated equilibrium, and on top of that you say that you were there when punctuated equilibrium was proposed just to keep belief in evolution. What a liar you are Pauline.

@ Pauline: "I'm not at Cambridge. I left in the 1980's hence my stupid and ignorant attempt at re-engaging with the subject, unfortunately with a gang of self-righteous bullies."

You're not so much engaging with a gang of "self-righteous bullies" as with real scientists whose education in science in general, and genetics in particular, far outweighs yours. A Cambridge undergraduate degree doesn't count for much if you haven't kept up in the field since obtaining it. If all I knew about paleontology was what I left Cambridge with in 1973 I'd be a pretty poor contestant on these boards.

And by the way: regarding there being no intermediate between the lungs of birds and reptiles, try Googling the work of Colleen Farmer, who has shown great similarity between alligator and bird lungs.

Christine wrote: "You're not so much engaging with a gang of "self-righteous bullies" as with real scientists whose education in science in general, and genetics in particular, far outweighs yours"Well as far as I know we have Piotr who is a linguist, Rumraket who is a lab assistant, Lutesuite who is a physiatrist, Steve with no apparent connection to science what so ever. In short I, don't think Pauline needs to worry about her degree, especially since most things discussed aren't exactly what you would describe as rocket science.

especially since most things discussed aren't exactly what you would describe as rocket science

No, they're biochemistry and evolutionary biology, which, if you get into the detail you should in order to have a good understanding, can be quite a bit more complex than most rocket science. The fact you haven't bothered to read, research and understand the complexities doesn't mean they don't exist or that they're not valuable knowledge.

"Pauline" also does not seem to know the correct meaning of the term "oxymoronic."

Hmmm ... there's another possibility. She might know what "oxymoronic" means but she thinks that entropy change can't be negative. That would make her scientifically illiterate but not necessarily illiterate in English.

I'm pretty sure that Andy's credentials far outweigh ... nah, they could not possibly outweigh anything. After what I have read from him, his "knowledge" and "understanding" of genetics in particular and of science in general greatly undermines any credentials he might hold.

Yes. It's hard to know what "Pauline" is thinking (If "thinking" is even the correct term for the process occuring in her faith-addled brain).

What creationists like "Pauline" don't realize is that the problem she raises exists for creationism as much as for evolution. If God had created humans specially, with perfect genomes devoid of any junk, then the mutation rates she cites cannot be explained. Human beings should have gone extinct long ago.

The fact that the large majority of the human genome consists of junk, of course, easily solves the problem of genetic load:

However, creationists reject the idea of junk DNA for theological reasons, so they remain unable to answer the problem that they themselves raise: How can the human genome tolerate such a frequency of mutations if all of the genome was "designed" to be functional?

It's not just junk dna. There were assumptions in Haldane's model that were wrong, as well as aspects of molecular evolution (genetic drift, neutral mutations, recombination, etc) that were not incorporated or incorrectly incorrectly incorporated into the model. What "Pauline" and the rest of the IDiots don't seem to grasp is that Haldane's model was A MODEL made in the 50's.

Aha! that makes sense now! You thought I believed that there was no junk DNA because I am a Creationist! Hence: "If God had created humans specially, with perfect genomes devoid of any junk, then..."What a silly mistake (among others)1. I am not a Creationist2. Unlike you I would never be so arrogant as to suppose that I would know whether an omnipotent God would put "junk" DNA into our genome.

Aha! that makes sense now! You thought I believed that there was no junk DNA because I am a Creationist!

No. We think you refuse to accept the concept of junk dna because you stated:

"Instead of questioning evolution, he proposed that most genetic information must be irrelevant and that evolution must be independent of selection!"

You can't accept junk dna and at the same time make that statement. Should be obvious for someone with genetics education. That statement also makes clear you don't understand Neutral Theory. Worse, the suggestion that Neutral Theory was some kind of attempt at "salvaging" TE without looking at "alternatives" is nonsense; NT and Nearly-NT are just the combination of various things that were already known, like genetic drift, and the nature of the genetic code. Your statement shows incomprehension more than anything else, and smacks of Creationist "logic", which justifies why I believe you're a poser. But as I said before, I'll give you the benefit of the doubt, for now.

Unlike you I would never be so arrogant as to suppose that I would know whether an omnipotent God would put "junk" DNA into our genome.

Ah, yes. But you have no problem presuming that I have an opinion on what God might or might not do if he had created humans, do you? If you can point out where I have stated such an opinion, please do so. Obviously (or so one would have thought) I was describing the creationist position, which consistently denies the existence of junk DNA since this would be inconsistent with the creationist concept of "design".

I shall point it out thank you. It was when you said: "If God had created humans specially, with perfect genomes devoid of any junk, then the mutation rates she cites cannot be explained."You assumed I am a Creationist (I'm not) and you assumed that God would make humans with perfect genomes (that's where you attempt to know what he (or she!) might do) and you assumed that I am in denial about "junk" DNA. What I have read about accumulating mutations and extinction rates and what I believe about entropy I actually have no problem with the genome being full of rubbish since the Fall (don't bite I'm not provoking you). When I was at Uni we thought a large amount of DNA was "junk" but I hear that new thinking is that it has been preserved so well that there must be some selective pressure on it? Don't swear just tell me if this is true you big bully. Some scientists are proposing non-coding uses for "junk" DNA?Here goes nothing - I'll press "publish" and duck.

You mistake the reason people think you deny the existence of junk DNA. It's not because of creationism. It's because you suppose that Haldane's dilemma makes evolution unlikely, even though if most of the genome is junk, there is no problem.

The "new thinking" you're talking about comes from two sources: 1) creationist nonsense and 2) ENCODE. You have been warned not to rely on the first, and if you search Larry's blog you will see many reasons not to rely on the second.

Note that "non-coding" and "junk" are not synonyms. We know of many bits of non-coding DNA that have functions, but they are not junk and have never been so considered, and they make up only a small percentage of the genome. There are also a few pieces of junk that, over the course of evolution, have acquired functions and thus become junk no longer. Again, those are a tiny, tiny proportion of the genome.

Short answer: most of your genome (90% or so) is clearly junk, based on many lines of evidence. And since that does much to resolve Haldane's dilemma, you should reconsider your objections to evolution on that score.

For crying out loud. Why can't you write more than a sentence without decending into abusive bullying?

You wrote: "If God..." then you made an assumption about HOW God would create humans (ie with perfect genomes devoid of any junk.) So you see the problem with your sentence was not the word "if". Now if you read back what I wrote you will see what I meant and the mistake you made by thinking I didn't understand the word "if". If you actually gave people the benefit of the doubt your life would be happier.I shall not make fun of the fact that you misunderstood me or attacked me unfairly, but just ask politely that you speak to me kindly please.

Boy, Pauline. You really are stupider than a sack of doorknobs, aren't you? Let me try to make it simple enough for you to understand, though that will be a formidable challenge.

Suppose I had written "If the world was only 6000 years old, then there would not have been enough time for the observed diversity of life to have arisen thru evolution." Now, from that, would it be correct to conclude that I believe the earth can only be 6000 years old?

Think carefully. It's not really that difficult.

Oh, and with your insulting comments towards others, and your blithe dismissal and misrepresentation of the work of dedicated scientists, you have long ago lost any right you might have to courteous treatment. You only deserve the same ridicule and scorn that is the desert of all creationists.

///Their model of intelligent design also has to account for the fact that humans are more similar to chimps/bonobos than to gorillas and all three are about the same genetic distance from orangutans.///

In 30% of its genome, gorilla is more closely related to humans or chimps than the latter are to each other.Why are humans closer to gorillas in a minor part of their genome, but closer to chimps in the rest?If looks & behavior implies genetic kinship, as Klinghoffer claims, then why are chimps closer to humans although their looks& behavior are a lot more similar to that of gorillas?Klinghoffer does not account for such details, he simply states that since apes & humans share resemblance, their DNA is expected to match. Moreover, if looks imply kinship, then whales must be genetically closer to sharks than to hippos. But we see the opposite!

There lies the most interesting bit I think, but nobody deigned commenting upon, despite over 100 comments. I know there's probably nothing to discuss, since 'conservative sexual habits' are down to almost null I guess. But that's also probably the reason why this thread occurs. Those human apes don't have enough sex.

Laurence A. Moran

Larry Moran is a Professor in the Department of Biochemistry at the University of Toronto. You can contact him by looking up his email address on the University of Toronto website.

Sandwalk

The Sandwalk is the path behind the home of Charles Darwin where he used to walk every day, thinking about science. You can see the path in the woods in the upper left-hand corner of this image.

Disclaimer

Some readers of this blog may be under the impression that my personal opinions represent the official position of Canada, the Province of Ontario, the City of Toronto, the University of Toronto, the Faculty of Medicine, or the Department of Biochemistry. All of these institutions, plus every single one of my colleagues, students, friends, and relatives, want you to know that I do not speak for them. You should also know that they don't speak for me.

Subscribe to Sandwalk

Quotations

The old argument of design in nature, as given by Paley, which formerly seemed to me to be so conclusive, fails, now that the law of natural selection has been discovered. We can no longer argue that, for instance, the beautiful hinge of a bivalve shell must have been made by an intelligent being, like the hinge of a door by man. There seems to be no more design in the variability of organic beings and in the action of natural selection, than in the course which the wind blows.Charles Darwin (c1880)Although I am fully convinced of the truth of the views given in this volume, I by no means expect to convince experienced naturalists whose minds are stocked with a multitude of facts all viewed, during a long course of years, from a point of view directly opposite to mine. It is so easy to hide our ignorance under such expressions as "plan of creation," "unity of design," etc., and to think that we give an explanation when we only restate a fact. Any one whose disposition leads him to attach more weight to unexplained difficulties than to the explanation of a certain number of facts will certainly reject the theory.

Charles Darwin (1859)Science reveals where religion conceals. Where religion purports to explain, it actually resorts to tautology. To assert that "God did it" is no more than an admission of ignorance dressed deceitfully as an explanation...

Quotations

The world is not inhabited exclusively by fools, and when a subject arouses intense interest, as this one has, something other than semantics is usually at stake.
Stephen Jay Gould (1982)
I have championed contingency, and will continue to do so, because its large realm and legitimate claims have been so poorly attended by evolutionary scientists who cannot discern the beat of this different drummer while their brains and ears remain tuned to only the sounds of general theory.
Stephen Jay Gould (2002) p.1339
The essence of Darwinism lies in its claim that natural selection creates the fit. Variation is ubiquitous and random in direction. It supplies raw material only. Natural selection directs the course of evolutionary change.
Stephen Jay Gould (1977)
Rudyard Kipling asked how the leopard got its spots, the rhino its wrinkled skin. He called his answers "just-so stories." When evolutionists try to explain form and behavior, they also tell just-so stories—and the agent is natural selection. Virtuosity in invention replaces testability as the criterion for acceptance.
Stephen Jay Gould (1980)
Since 'change of gene frequencies in populations' is the 'official' definition of evolution, randomness has transgressed Darwin's border and asserted itself as an agent of evolutionary change.
Stephen Jay Gould (1983) p.335
The first commandment for all versions of NOMA might be summarized by stating: "Thou shalt not mix the magisteria by claiming that God directly ordains important events in the history of nature by special interference knowable only through revelation and not accessible to science." In common parlance, we refer to such special interference as "miracle"—operationally defined as a unique and temporary suspension of natural law to reorder the facts of nature by divine fiat.
Stephen Jay Gould (1999) p.84

Quotations

My own view is that conclusions about the evolution of human behavior should be based on research at least as rigorous as that used in studying nonhuman animals. And if you read the animal behavior journals, you'll see that this requirement sets the bar pretty high, so that many assertions about evolutionary psychology sink without a trace.

Jerry Coyne
Why Evolution Is TrueI once made the remark that two things disappeared in 1990: one was communism, the other was biochemistry and that only one of them should be allowed to come back.

Sydney Brenner
TIBS Dec. 2000
It is naïve to think that if a species' environment changes the species must adapt or else become extinct.... Just as a changed environment need not set in motion selection for new adaptations, new adaptations may evolve in an unchanging environment if new mutations arise that are superior to any pre-existing variations

Douglas Futuyma
One of the most frightening things in the Western world, and in this country in particular, is the number of people who believe in things that are scientifically false. If someone tells me that the earth is less than 10,000 years old, in my opinion he should see a psychiatrist.

Francis Crick
There will be no difficulty in computers being adapted to biology. There will be luddites. But they will be buried.

Sydney Brenner
An atheist before Darwin could have said, following Hume: 'I have no explanation for complex biological design. All I know is that God isn't a good explanation, so we must wait and hope that somebody comes up with a better one.' I can't help feeling that such a position, though logically sound, would have left one feeling pretty unsatisfied, and that although atheism might have been logically tenable before Darwin, Darwin made it possible to be an intellectually fulfilled atheist

Richard Dawkins
Another curious aspect of the theory of evolution is that everybody thinks he understand it. I mean philosophers, social scientists, and so on. While in fact very few people understand it, actually as it stands, even as it stood when Darwin expressed it, and even less as we now may be able to understand it in biology.

Jacques Monod
The false view of evolution as a process of global optimizing has been applied literally by engineers who, taken in by a mistaken metaphor, have attempted to find globally optimal solutions to design problems by writing programs that model evolution by natural selection.